TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data [version 1; peer review: 1 approved, 1 approved with reservations]

Tiago Chedraoui Silva; Antonio Colaprico; Catharina Olsen; Tathiane M. Malta; Gianluca Bontempi; Michele Ceccarelli; Benjamin P. Berman; Houtan Noushmehr

doi:10.12688/F1000RESEARCH.14197.1

TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data [version 1; peer review: 1 approved, 1 approved with reservations]

Tiago Chedraoui Silva
, Antonio Colaprico
, Catharina Olsen
, Tathiane M. Malta
, Gianluca Bontempi
, Michele Ceccarelli
, Benjamin P. Berman
, Houtan Noushmehr

Research output: Contribution to journal › Article › peer-review

Abstract

The GDC (Genomic Data Commons) data portal provides users with data from cancer genomics studies. Recently, we developed the R/Bioconductor TCGAbiolinks package, which allows users to search, download and prepare cancer genomics data for integrative data analysis. The use of this package requires users to have advanced knowledge of R thus limiting the number of users. To overcome this obstacle and improve the accessibility of the package by a wider range of users, we developed a graphical user interface (GUI) using Shiny available through the package TCGAbiolinksGUI. The TCGAbiolinksGUI package is freely available within the Bioconductor project at http://bioconductor.org/packages/TCGAbiolinksGUI/. Links to the GitHub repository, a demo version of the tool, a docker image and PDF/video tutorials are available from the TCGAbiolinksGUI site.

Original language	American English
Article number	439
Journal	F1000Research
Volume	7
DOIs	https://doi.org/10.12688/F1000RESEARCH.14197.1
State	Published - 2018
Externally published	Yes

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Bioinformatics
Cancer
Epigenomics
Genomics
TCGA

ASJC Scopus subject areas

General Biochemistry,Genetics and Molecular Biology
General Immunology and Microbiology
Pharmacology, Toxicology and Pharmaceutics(all)

Access to Document

10.12688/F1000RESEARCH.14197.1

Cite this

@article{999a4753163c43828d6bc6598e2cd70a,

title = "TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data [version 1; peer review: 1 approved, 1 approved with reservations]",

abstract = "The GDC (Genomic Data Commons) data portal provides users with data from cancer genomics studies. Recently, we developed the R/Bioconductor TCGAbiolinks package, which allows users to search, download and prepare cancer genomics data for integrative data analysis. The use of this package requires users to have advanced knowledge of R thus limiting the number of users. To overcome this obstacle and improve the accessibility of the package by a wider range of users, we developed a graphical user interface (GUI) using Shiny available through the package TCGAbiolinksGUI. The TCGAbiolinksGUI package is freely available within the Bioconductor project at http://bioconductor.org/packages/TCGAbiolinksGUI/. Links to the GitHub repository, a demo version of the tool, a docker image and PDF/video tutorials are available from the TCGAbiolinksGUI site.",

keywords = "Bioinformatics, Cancer, Epigenomics, Genomics, TCGA",

author = "Silva, \{Tiago Chedraoui\} and Antonio Colaprico and Catharina Olsen and Malta, \{Tathiane M.\} and Gianluca Bontempi and Michele Ceccarelli and Berman, \{Benjamin P.\} and Houtan Noushmehr",

note = "Funding Information: This work has been supported by a grant from Henry Ford Hospital (H.N.) and by the S{\~a}o Paulo Research Foundation (FAPESP) (2016/01389-7 to T.C.S. \& H.N. and 2015/07925-5 to H.N.) the BridgeIRIS project, funded by INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium, and by GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR (T100914F to A.C., C.O.\& G.B.). T.C.S. and B.P.B. were supported by the NCI Informatics Technology for Cancer Research program, NIH/NCI grant 1U01CA184826 and Genomic Data Analysis Network NIH/NCI grant 1U24CA210969. Funding Information: This work has been supported by a grant from Henry Ford Hospital (H.N.) and by the S?o Paulo Research Foundation (FAPESP) (2016/01389-7 to T.C.S. \& H.N. and 2015/07925-5 to H.N.) the BridgeIRIS project, funded by INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium, and by GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR (T100914F to A.C., C.O.\& G.B.). T.C.S. and B.P.B. were supported by the NCI Informatics Technology for Cancer Research program, NIH/NCI grant 1U01CA184826 and Genomic Data Analysis Network NIH/NCI grant 1U24CA210969. Funding Information: Grant information: This work has been supported by a grant from Henry Ford Hospital (H.N.) and by the S{\~a}o Paulo Research Foundation (FAPESP) (2016/01389-7 to T.C.S. \& H.N. and 2015/07925-5 to H.N.) the BridgeIRIS project, funded by INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium, and by GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR (T100914F to A.C., C.O.\& G.B.). T.C.S. and B.P.B. were supported by the NCI Informatics Technology for Cancer Research program, NIH/NCI grant 1U01CA184826 and Genomic Data Analysis Network NIH/NCI grant 1U24CA210969 Publisher Copyright: {\textcopyright} 2018 Silva TC et al.",

year = "2018",

doi = "10.12688/F1000RESEARCH.14197.1",

language = "American English",

volume = "7",

journal = "F1000Research",

issn = "2046-1402",

publisher = "F1000 Research Ltd.",

}

TY - JOUR

T1 - TCGAbiolinksGUI

T2 - A graphical user interface to analyze cancer molecular and clinical data [version 1; peer review: 1 approved, 1 approved with reservations]

AU - Silva, Tiago Chedraoui

AU - Colaprico, Antonio

AU - Olsen, Catharina

AU - Malta, Tathiane M.

AU - Bontempi, Gianluca

AU - Ceccarelli, Michele

AU - Berman, Benjamin P.

AU - Noushmehr, Houtan

N1 - Funding Information: This work has been supported by a grant from Henry Ford Hospital (H.N.) and by the São Paulo Research Foundation (FAPESP) (2016/01389-7 to T.C.S. & H.N. and 2015/07925-5 to H.N.) the BridgeIRIS project, funded by INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium, and by GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR (T100914F to A.C., C.O.& G.B.). T.C.S. and B.P.B. were supported by the NCI Informatics Technology for Cancer Research program, NIH/NCI grant 1U01CA184826 and Genomic Data Analysis Network NIH/NCI grant 1U24CA210969. Funding Information: This work has been supported by a grant from Henry Ford Hospital (H.N.) and by the S?o Paulo Research Foundation (FAPESP) (2016/01389-7 to T.C.S. & H.N. and 2015/07925-5 to H.N.) the BridgeIRIS project, funded by INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium, and by GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR (T100914F to A.C., C.O.& G.B.). T.C.S. and B.P.B. were supported by the NCI Informatics Technology for Cancer Research program, NIH/NCI grant 1U01CA184826 and Genomic Data Analysis Network NIH/NCI grant 1U24CA210969. Funding Information: Grant information: This work has been supported by a grant from Henry Ford Hospital (H.N.) and by the São Paulo Research Foundation (FAPESP) (2016/01389-7 to T.C.S. & H.N. and 2015/07925-5 to H.N.) the BridgeIRIS project, funded by INNOVIRIS, Region de Bruxelles Capitale, Brussels, Belgium, and by GENomic profiling of Gastrointestinal Inflammatory-Sensitive CANcers (GENGISCAN), Belgian FNRS PDR (T100914F to A.C., C.O.& G.B.). T.C.S. and B.P.B. were supported by the NCI Informatics Technology for Cancer Research program, NIH/NCI grant 1U01CA184826 and Genomic Data Analysis Network NIH/NCI grant 1U24CA210969 Publisher Copyright: © 2018 Silva TC et al.

PY - 2018

Y1 - 2018

N2 - The GDC (Genomic Data Commons) data portal provides users with data from cancer genomics studies. Recently, we developed the R/Bioconductor TCGAbiolinks package, which allows users to search, download and prepare cancer genomics data for integrative data analysis. The use of this package requires users to have advanced knowledge of R thus limiting the number of users. To overcome this obstacle and improve the accessibility of the package by a wider range of users, we developed a graphical user interface (GUI) using Shiny available through the package TCGAbiolinksGUI. The TCGAbiolinksGUI package is freely available within the Bioconductor project at http://bioconductor.org/packages/TCGAbiolinksGUI/. Links to the GitHub repository, a demo version of the tool, a docker image and PDF/video tutorials are available from the TCGAbiolinksGUI site.

AB - The GDC (Genomic Data Commons) data portal provides users with data from cancer genomics studies. Recently, we developed the R/Bioconductor TCGAbiolinks package, which allows users to search, download and prepare cancer genomics data for integrative data analysis. The use of this package requires users to have advanced knowledge of R thus limiting the number of users. To overcome this obstacle and improve the accessibility of the package by a wider range of users, we developed a graphical user interface (GUI) using Shiny available through the package TCGAbiolinksGUI. The TCGAbiolinksGUI package is freely available within the Bioconductor project at http://bioconductor.org/packages/TCGAbiolinksGUI/. Links to the GitHub repository, a demo version of the tool, a docker image and PDF/video tutorials are available from the TCGAbiolinksGUI site.

KW - Bioinformatics

KW - Cancer

KW - Epigenomics

KW - Genomics

KW - TCGA

UR - https://www.scopus.com/pages/publications/85072120726

U2 - 10.12688/F1000RESEARCH.14197.1

DO - 10.12688/F1000RESEARCH.14197.1

M3 - Article

SN - 2046-1402

VL - 7

JO - F1000Research

JF - F1000Research

M1 - 439

ER -

TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data [version 1; peer review: 1 approved, 1 approved with reservations]

Abstract

UN SDGs

Keywords

ASJC Scopus subject areas

Access to Document

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